Actual source code: swarmpic.c
1: #define PETSCDM_DLL
2: #include <petsc/private/dmswarmimpl.h>
3: #include <petscsf.h>
4: #include <petscdmda.h>
5: #include <petscdmplex.h>
6: #include <petscdt.h>
7: #include "../src/dm/impls/swarm/data_bucket.h"
9: #include <petsc/private/petscfeimpl.h>
11: /* Coordinate insertition/addition API */
12: /*@C
13: DMSwarmSetPointsUniformCoordinates - Set point coordinates in a `DMSWARM` on a regular (ijk) grid
15: Collective
17: Input Parameters:
18: + dm - the `DMSWARM`
19: . min - minimum coordinate values in the x, y, z directions (array of length dim)
20: . max - maximum coordinate values in the x, y, z directions (array of length dim)
21: . npoints - number of points in each spatial direction (array of length dim)
22: - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
24: Level: beginner
26: Notes:
27: When using mode = `INSERT_VALUES`, this method will reset the number of particles in the `DMSWARM`
28: to be npoints[0]*npoints[1] (2D) or npoints[0]*npoints[1]*npoints[2] (3D). When using mode = `ADD_VALUES`,
29: new points will be appended to any already existing in the `DMSWARM`
31: .seealso: `DM`, `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
32: @*/
33: PETSC_EXTERN PetscErrorCode DMSwarmSetPointsUniformCoordinates(DM dm, PetscReal min[], PetscReal max[], PetscInt npoints[], InsertMode mode)
34: {
35: PetscReal gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
36: PetscReal gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
37: PetscInt i, j, k, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
38: Vec coorlocal;
39: const PetscScalar *_coor;
40: DM celldm;
41: PetscReal dx[3];
42: PetscInt _npoints[] = {0, 0, 1};
43: Vec pos;
44: PetscScalar *_pos;
45: PetscReal *swarm_coor;
46: PetscInt *swarm_cellid;
47: PetscSF sfcell = NULL;
48: const PetscSFNode *LA_sfcell;
50: PetscFunctionBegin;
51: DMSWARMPICVALID(dm);
52: PetscCall(DMSwarmGetCellDM(dm, &celldm));
53: PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal));
54: PetscCall(VecGetSize(coorlocal, &N));
55: PetscCall(VecGetBlockSize(coorlocal, &bs));
56: N = N / bs;
57: PetscCall(VecGetArrayRead(coorlocal, &_coor));
58: for (i = 0; i < N; i++) {
59: for (b = 0; b < bs; b++) {
60: gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b]));
61: gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b]));
62: }
63: }
64: PetscCall(VecRestoreArrayRead(coorlocal, &_coor));
66: for (b = 0; b < bs; b++) {
67: if (npoints[b] > 1) {
68: dx[b] = (max[b] - min[b]) / ((PetscReal)(npoints[b] - 1));
69: } else {
70: dx[b] = 0.0;
71: }
72: _npoints[b] = npoints[b];
73: }
75: /* determine number of points living in the bounding box */
76: n_estimate = 0;
77: for (k = 0; k < _npoints[2]; k++) {
78: for (j = 0; j < _npoints[1]; j++) {
79: for (i = 0; i < _npoints[0]; i++) {
80: PetscReal xp[] = {0.0, 0.0, 0.0};
81: PetscInt ijk[3];
82: PetscBool point_inside = PETSC_TRUE;
84: ijk[0] = i;
85: ijk[1] = j;
86: ijk[2] = k;
87: for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
88: for (b = 0; b < bs; b++) {
89: if (xp[b] < gmin[b]) point_inside = PETSC_FALSE;
90: if (xp[b] > gmax[b]) point_inside = PETSC_FALSE;
91: }
92: if (point_inside) n_estimate++;
93: }
94: }
95: }
97: /* create candidate list */
98: PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
99: PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
100: PetscCall(VecSetBlockSize(pos, bs));
101: PetscCall(VecSetFromOptions(pos));
102: PetscCall(VecGetArray(pos, &_pos));
104: n_estimate = 0;
105: for (k = 0; k < _npoints[2]; k++) {
106: for (j = 0; j < _npoints[1]; j++) {
107: for (i = 0; i < _npoints[0]; i++) {
108: PetscReal xp[] = {0.0, 0.0, 0.0};
109: PetscInt ijk[3];
110: PetscBool point_inside = PETSC_TRUE;
112: ijk[0] = i;
113: ijk[1] = j;
114: ijk[2] = k;
115: for (b = 0; b < bs; b++) xp[b] = min[b] + ijk[b] * dx[b];
116: for (b = 0; b < bs; b++) {
117: if (xp[b] < gmin[b]) point_inside = PETSC_FALSE;
118: if (xp[b] > gmax[b]) point_inside = PETSC_FALSE;
119: }
120: if (point_inside) {
121: for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = xp[b];
122: n_estimate++;
123: }
124: }
125: }
126: }
127: PetscCall(VecRestoreArray(pos, &_pos));
129: /* locate points */
130: PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
131: PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
132: n_found = 0;
133: for (p = 0; p < n_estimate; p++) {
134: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
135: }
137: /* adjust size */
138: if (mode == ADD_VALUES) {
139: PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
140: n_new_est = n_curr + n_found;
141: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
142: }
143: if (mode == INSERT_VALUES) {
144: n_curr = 0;
145: n_new_est = n_found;
146: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
147: }
149: /* initialize new coords, cell owners, pid */
150: PetscCall(VecGetArrayRead(pos, &_coor));
151: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
152: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
153: n_found = 0;
154: for (p = 0; p < n_estimate; p++) {
155: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
156: for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
157: swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
158: n_found++;
159: }
160: }
161: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
162: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
163: PetscCall(VecRestoreArrayRead(pos, &_coor));
165: PetscCall(PetscSFDestroy(&sfcell));
166: PetscCall(VecDestroy(&pos));
167: PetscFunctionReturn(PETSC_SUCCESS);
168: }
170: /*@C
171: DMSwarmSetPointCoordinates - Set point coordinates in a `DMSWARM` from a user defined list
173: Collective
175: Input Parameters:
176: + dm - the `DMSWARM`
177: . npoints - the number of points to insert
178: . coor - the coordinate values
179: . redundant - if set to `PETSC_TRUE`, it is assumed that `npoints` and `coor` are only valid on rank 0 and should be broadcast to other ranks
180: - mode - indicates whether to append points to the swarm (`ADD_VALUES`), or over-ride existing points (`INSERT_VALUES`)
182: Level: beginner
184: Notes:
185: If the user has specified `redundant` as `PETSC_FALSE`, the cell `DM` will attempt to locate the coordinates provided by `coor` within
186: its sub-domain. If they any values within `coor` are not located in the sub-domain, they will be ignored and will not get
187: added to the `DMSWARM`.
189: .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`, `DMSwarmSetPointsUniformCoordinates()`
190: @*/
191: PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinates(DM dm, PetscInt npoints, PetscReal coor[], PetscBool redundant, InsertMode mode)
192: {
193: PetscReal gmin[] = {PETSC_MAX_REAL, PETSC_MAX_REAL, PETSC_MAX_REAL};
194: PetscReal gmax[] = {PETSC_MIN_REAL, PETSC_MIN_REAL, PETSC_MIN_REAL};
195: PetscInt i, N, bs, b, n_estimate, n_curr, n_new_est, p, n_found;
196: Vec coorlocal;
197: const PetscScalar *_coor;
198: DM celldm;
199: Vec pos;
200: PetscScalar *_pos;
201: PetscReal *swarm_coor;
202: PetscInt *swarm_cellid;
203: PetscSF sfcell = NULL;
204: const PetscSFNode *LA_sfcell;
205: PetscReal *my_coor;
206: PetscInt my_npoints;
207: PetscMPIInt rank;
208: MPI_Comm comm;
210: PetscFunctionBegin;
211: DMSWARMPICVALID(dm);
212: PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
213: PetscCallMPI(MPI_Comm_rank(comm, &rank));
215: PetscCall(DMSwarmGetCellDM(dm, &celldm));
216: PetscCall(DMGetCoordinatesLocal(celldm, &coorlocal));
217: PetscCall(VecGetSize(coorlocal, &N));
218: PetscCall(VecGetBlockSize(coorlocal, &bs));
219: N = N / bs;
220: PetscCall(VecGetArrayRead(coorlocal, &_coor));
221: for (i = 0; i < N; i++) {
222: for (b = 0; b < bs; b++) {
223: gmin[b] = PetscMin(gmin[b], PetscRealPart(_coor[bs * i + b]));
224: gmax[b] = PetscMax(gmax[b], PetscRealPart(_coor[bs * i + b]));
225: }
226: }
227: PetscCall(VecRestoreArrayRead(coorlocal, &_coor));
229: /* broadcast points from rank 0 if requested */
230: if (redundant) {
231: my_npoints = npoints;
232: PetscCallMPI(MPI_Bcast(&my_npoints, 1, MPIU_INT, 0, comm));
234: if (rank > 0) { /* allocate space */
235: PetscCall(PetscMalloc1(bs * my_npoints, &my_coor));
236: } else {
237: my_coor = coor;
238: }
239: PetscCallMPI(MPI_Bcast(my_coor, bs * my_npoints, MPIU_REAL, 0, comm));
240: } else {
241: my_npoints = npoints;
242: my_coor = coor;
243: }
245: /* determine the number of points living in the bounding box */
246: n_estimate = 0;
247: for (i = 0; i < my_npoints; i++) {
248: PetscBool point_inside = PETSC_TRUE;
250: for (b = 0; b < bs; b++) {
251: if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
252: if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
253: }
254: if (point_inside) n_estimate++;
255: }
257: /* create candidate list */
258: PetscCall(VecCreate(PETSC_COMM_SELF, &pos));
259: PetscCall(VecSetSizes(pos, bs * n_estimate, PETSC_DECIDE));
260: PetscCall(VecSetBlockSize(pos, bs));
261: PetscCall(VecSetFromOptions(pos));
262: PetscCall(VecGetArray(pos, &_pos));
264: n_estimate = 0;
265: for (i = 0; i < my_npoints; i++) {
266: PetscBool point_inside = PETSC_TRUE;
268: for (b = 0; b < bs; b++) {
269: if (my_coor[bs * i + b] < gmin[b]) point_inside = PETSC_FALSE;
270: if (my_coor[bs * i + b] > gmax[b]) point_inside = PETSC_FALSE;
271: }
272: if (point_inside) {
273: for (b = 0; b < bs; b++) _pos[bs * n_estimate + b] = my_coor[bs * i + b];
274: n_estimate++;
275: }
276: }
277: PetscCall(VecRestoreArray(pos, &_pos));
279: /* locate points */
280: PetscCall(DMLocatePoints(celldm, pos, DM_POINTLOCATION_NONE, &sfcell));
282: PetscCall(PetscSFGetGraph(sfcell, NULL, NULL, NULL, &LA_sfcell));
283: n_found = 0;
284: for (p = 0; p < n_estimate; p++) {
285: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) n_found++;
286: }
288: /* adjust size */
289: if (mode == ADD_VALUES) {
290: PetscCall(DMSwarmGetLocalSize(dm, &n_curr));
291: n_new_est = n_curr + n_found;
292: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
293: }
294: if (mode == INSERT_VALUES) {
295: n_curr = 0;
296: n_new_est = n_found;
297: PetscCall(DMSwarmSetLocalSizes(dm, n_new_est, -1));
298: }
300: /* initialize new coords, cell owners, pid */
301: PetscCall(VecGetArrayRead(pos, &_coor));
302: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
303: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
304: n_found = 0;
305: for (p = 0; p < n_estimate; p++) {
306: if (LA_sfcell[p].index != DMLOCATEPOINT_POINT_NOT_FOUND) {
307: for (b = 0; b < bs; b++) swarm_coor[bs * (n_curr + n_found) + b] = PetscRealPart(_coor[bs * p + b]);
308: swarm_cellid[n_curr + n_found] = LA_sfcell[p].index;
309: n_found++;
310: }
311: }
312: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
313: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_coor, NULL, NULL, (void **)&swarm_coor));
314: PetscCall(VecRestoreArrayRead(pos, &_coor));
316: if (redundant) {
317: if (rank > 0) PetscCall(PetscFree(my_coor));
318: }
319: PetscCall(PetscSFDestroy(&sfcell));
320: PetscCall(VecDestroy(&pos));
321: PetscFunctionReturn(PETSC_SUCCESS);
322: }
324: extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_DA(DM, DM, DMSwarmPICLayoutType, PetscInt);
325: extern PetscErrorCode private_DMSwarmInsertPointsUsingCellDM_PLEX(DM, DM, DMSwarmPICLayoutType, PetscInt);
327: /*@C
328: DMSwarmInsertPointsUsingCellDM - Insert point coordinates within each cell
330: Not Collective
332: Input Parameters:
333: + dm - the `DMSWARM`
334: . layout_type - method used to fill each cell with the cell `DM`
335: - fill_param - parameter controlling how many points per cell are added (the meaning of this parameter is dependent on the layout type)
337: Level: beginner
339: Notes:
340: The insert method will reset any previous defined points within the `DMSWARM`.
342: When using a `DMDA` both 2D and 3D are supported for all layout types provided you are using `DMDA_ELEMENT_Q1`.
344: When using a `DMPLEX` the following case are supported\:
345: .vb
346: (i) DMSWARMPIC_LAYOUT_REGULAR: 2D (triangle),
347: (ii) DMSWARMPIC_LAYOUT_GAUSS: 2D and 3D provided the cell is a tri/tet or a quad/hex,
348: (iii) DMSWARMPIC_LAYOUT_SUBDIVISION: 2D and 3D for quad/hex and 2D tri.
349: .ve
351: .seealso: `DMSWARM`, `DMSwarmPICLayoutType`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
352: @*/
353: PETSC_EXTERN PetscErrorCode DMSwarmInsertPointsUsingCellDM(DM dm, DMSwarmPICLayoutType layout_type, PetscInt fill_param)
354: {
355: DM celldm;
356: PetscBool isDA, isPLEX;
358: PetscFunctionBegin;
359: DMSWARMPICVALID(dm);
360: PetscCall(DMSwarmGetCellDM(dm, &celldm));
361: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
362: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
363: if (isDA) {
364: PetscCall(private_DMSwarmInsertPointsUsingCellDM_DA(dm, celldm, layout_type, fill_param));
365: } else if (isPLEX) {
366: PetscCall(private_DMSwarmInsertPointsUsingCellDM_PLEX(dm, celldm, layout_type, fill_param));
367: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
368: PetscFunctionReturn(PETSC_SUCCESS);
369: }
371: extern PetscErrorCode private_DMSwarmSetPointCoordinatesCellwise_PLEX(DM, DM, PetscInt, PetscReal *);
373: /*@C
374: DMSwarmSetPointCoordinatesCellwise - Insert point coordinates (defined over the reference cell) within each cell
376: Not Collective
378: Input Parameters:
379: + dm - the `DMSWARM`
380: . npoints - the number of points to insert in each cell
381: - xi - the coordinates (defined in the local coordinate system for each cell) to insert
383: Level: beginner
385: Notes:
386: The method will reset any previous defined points within the `DMSWARM`.
387: Only supported for `DMPLEX`. If you are using a `DMDA` it is recommended to either use
388: `DMSwarmInsertPointsUsingCellDM()`, or extract and set the coordinates yourself the following code
389: .vb
390: PetscReal *coor;
391: DMSwarmGetField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
392: // user code to define the coordinates here
393: DMSwarmRestoreField(dm,DMSwarmPICField_coor,NULL,NULL,(void**)&coor);
394: .ve
396: .seealso: `DMSWARM`, `DMSwarmSetCellDM()`, `DMSwarmInsertPointsUsingCellDM()`
397: @*/
398: PETSC_EXTERN PetscErrorCode DMSwarmSetPointCoordinatesCellwise(DM dm, PetscInt npoints, PetscReal xi[])
399: {
400: DM celldm;
401: PetscBool isDA, isPLEX;
403: PetscFunctionBegin;
404: DMSWARMPICVALID(dm);
405: PetscCall(DMSwarmGetCellDM(dm, &celldm));
406: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isDA));
407: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isPLEX));
408: PetscCheck(!isDA, PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMPLEX. Recommended you use DMSwarmInsertPointsUsingCellDM()");
409: if (isPLEX) {
410: PetscCall(private_DMSwarmSetPointCoordinatesCellwise_PLEX(dm, celldm, npoints, xi));
411: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Only supported for cell DMs of type DMDA and DMPLEX");
412: PetscFunctionReturn(PETSC_SUCCESS);
413: }
415: /*@C
416: DMSwarmCreatePointPerCellCount - Count the number of points within all cells in the cell DM
418: Not Collective
420: Input Parameter:
421: . dm - the `DMSWARM`
423: Output Parameters:
424: + ncells - the number of cells in the cell `DM` (optional argument, pass `NULL` to ignore)
425: - count - array of length ncells containing the number of points per cell
427: Level: beginner
429: Notes:
430: The array count is allocated internally and must be free'd by the user.
432: .seealso: `DMSWARM`, `DMSwarmSetType()`, `DMSwarmSetCellDM()`, `DMSwarmType`
433: @*/
434: PETSC_EXTERN PetscErrorCode DMSwarmCreatePointPerCellCount(DM dm, PetscInt *ncells, PetscInt **count)
435: {
436: PetscBool isvalid;
437: PetscInt nel;
438: PetscInt *sum;
440: PetscFunctionBegin;
441: PetscCall(DMSwarmSortGetIsValid(dm, &isvalid));
442: nel = 0;
443: if (isvalid) {
444: PetscInt e;
446: PetscCall(DMSwarmSortGetSizes(dm, &nel, NULL));
448: PetscCall(PetscMalloc1(nel, &sum));
449: for (e = 0; e < nel; e++) PetscCall(DMSwarmSortGetNumberOfPointsPerCell(dm, e, &sum[e]));
450: } else {
451: DM celldm;
452: PetscBool isda, isplex, isshell;
453: PetscInt p, npoints;
454: PetscInt *swarm_cellid;
456: /* get the number of cells */
457: PetscCall(DMSwarmGetCellDM(dm, &celldm));
458: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMDA, &isda));
459: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMPLEX, &isplex));
460: PetscCall(PetscObjectTypeCompare((PetscObject)celldm, DMSHELL, &isshell));
461: if (isda) {
462: PetscInt _nel, _npe;
463: const PetscInt *_element;
465: PetscCall(DMDAGetElements(celldm, &_nel, &_npe, &_element));
466: nel = _nel;
467: PetscCall(DMDARestoreElements(celldm, &_nel, &_npe, &_element));
468: } else if (isplex) {
469: PetscInt ps, pe;
471: PetscCall(DMPlexGetHeightStratum(celldm, 0, &ps, &pe));
472: nel = pe - ps;
473: } else if (isshell) {
474: PetscErrorCode (*method_DMShellGetNumberOfCells)(DM, PetscInt *);
476: PetscCall(PetscObjectQueryFunction((PetscObject)celldm, "DMGetNumberOfCells_C", &method_DMShellGetNumberOfCells));
477: if (method_DMShellGetNumberOfCells) {
478: PetscCall(method_DMShellGetNumberOfCells(celldm, &nel));
479: } else
480: SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for the DMSHELL object. User must provide a method via PetscObjectComposeFunction( (PetscObject)shelldm, \"DMGetNumberOfCells_C\", your_function_to_compute_number_of_cells);");
481: } else SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Cannot determine the number of cells for a DM not of type DA, PLEX or SHELL");
483: PetscCall(PetscMalloc1(nel, &sum));
484: PetscCall(PetscArrayzero(sum, nel));
485: PetscCall(DMSwarmGetLocalSize(dm, &npoints));
486: PetscCall(DMSwarmGetField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
487: for (p = 0; p < npoints; p++) {
488: if (swarm_cellid[p] != DMLOCATEPOINT_POINT_NOT_FOUND) sum[swarm_cellid[p]]++;
489: }
490: PetscCall(DMSwarmRestoreField(dm, DMSwarmPICField_cellid, NULL, NULL, (void **)&swarm_cellid));
491: }
492: if (ncells) *ncells = nel;
493: *count = sum;
494: PetscFunctionReturn(PETSC_SUCCESS);
495: }
497: /*@
498: DMSwarmGetNumSpecies - Get the number of particle species
500: Not Collective
502: Input Parameter:
503: . sw - the `DMSWARM`
505: Output Parameters:
506: . Ns - the number of species
508: Level: intermediate
510: .seealso: `DMSWARM`, `DMSwarmSetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
511: @*/
512: PetscErrorCode DMSwarmGetNumSpecies(DM sw, PetscInt *Ns)
513: {
514: DM_Swarm *swarm = (DM_Swarm *)sw->data;
516: PetscFunctionBegin;
517: *Ns = swarm->Ns;
518: PetscFunctionReturn(PETSC_SUCCESS);
519: }
521: /*@
522: DMSwarmSetNumSpecies - Set the number of particle species
524: Not Collective
526: Input Parameters:
527: + sw - the `DMSWARM`
528: - Ns - the number of species
530: Level: intermediate
532: .seealso: `DMSWARM`, `DMSwarmGetNumSpecies()`, `DMSwarmSetType()`, `DMSwarmType`
533: @*/
534: PetscErrorCode DMSwarmSetNumSpecies(DM sw, PetscInt Ns)
535: {
536: DM_Swarm *swarm = (DM_Swarm *)sw->data;
538: PetscFunctionBegin;
539: swarm->Ns = Ns;
540: PetscFunctionReturn(PETSC_SUCCESS);
541: }
543: /*@C
544: DMSwarmGetCoordinateFunction - Get the function setting initial particle positions, if it exists
546: Not Collective
548: Input Parameter:
549: . sw - the `DMSWARM`
551: Output Parameter:
552: . coordFunc - the function setting initial particle positions, or `NULL`
554: Level: intermediate
556: .seealso: `DMSWARM`, `DMSwarmSetCoordinateFunction()`, `DMSwarmGetVelocityFunction()`, `DMSwarmInitializeCoordinates()`
557: @*/
558: PetscErrorCode DMSwarmGetCoordinateFunction(DM sw, PetscSimplePointFunc *coordFunc)
559: {
560: DM_Swarm *swarm = (DM_Swarm *)sw->data;
562: PetscFunctionBegin;
564: PetscAssertPointer(coordFunc, 2);
565: *coordFunc = swarm->coordFunc;
566: PetscFunctionReturn(PETSC_SUCCESS);
567: }
569: /*@C
570: DMSwarmSetCoordinateFunction - Set the function setting initial particle positions
572: Not Collective
574: Input Parameters:
575: + sw - the `DMSWARM`
576: - coordFunc - the function setting initial particle positions
578: Level: intermediate
580: .seealso: `DMSWARM`, `DMSwarmGetCoordinateFunction()`, `DMSwarmSetVelocityFunction()`, `DMSwarmInitializeCoordinates()`
581: @*/
582: PetscErrorCode DMSwarmSetCoordinateFunction(DM sw, PetscSimplePointFunc coordFunc)
583: {
584: DM_Swarm *swarm = (DM_Swarm *)sw->data;
586: PetscFunctionBegin;
589: swarm->coordFunc = coordFunc;
590: PetscFunctionReturn(PETSC_SUCCESS);
591: }
593: /*@C
594: DMSwarmGetVelocityFunction - Get the function setting initial particle velocities, if it exists
596: Not Collective
598: Input Parameter:
599: . sw - the `DMSWARM`
601: Output Parameter:
602: . velFunc - the function setting initial particle velocities, or `NULL`
604: Level: intermediate
606: .seealso: `DMSWARM`, `DMSwarmSetVelocityFunction()`, `DMSwarmGetCoordinateFunction()`, `DMSwarmInitializeVelocities()`
607: @*/
608: PetscErrorCode DMSwarmGetVelocityFunction(DM sw, PetscSimplePointFunc *velFunc)
609: {
610: DM_Swarm *swarm = (DM_Swarm *)sw->data;
612: PetscFunctionBegin;
614: PetscAssertPointer(velFunc, 2);
615: *velFunc = swarm->velFunc;
616: PetscFunctionReturn(PETSC_SUCCESS);
617: }
619: /*@C
620: DMSwarmSetVelocityFunction - Set the function setting initial particle velocities
622: Not Collective
624: Input Parameters:
625: + sw - the `DMSWARM`
626: - velFunc - the function setting initial particle velocities
628: Level: intermediate
630: .seealso: `DMSWARM`, `DMSwarmGetVelocityFunction()`, `DMSwarmSetCoordinateFunction()`, `DMSwarmInitializeVelocities()`
631: @*/
632: PetscErrorCode DMSwarmSetVelocityFunction(DM sw, PetscSimplePointFunc velFunc)
633: {
634: DM_Swarm *swarm = (DM_Swarm *)sw->data;
636: PetscFunctionBegin;
639: swarm->velFunc = velFunc;
640: PetscFunctionReturn(PETSC_SUCCESS);
641: }
643: /*@C
644: DMSwarmComputeLocalSize - Compute the local number and distribution of particles based upon a density function
646: Not Collective
648: Input Parameters:
649: + sw - The `DMSWARM`
650: . N - The target number of particles
651: - density - The density field for the particle layout, normalized to unity
653: Level: advanced
655: Note:
656: One particle will be created for each species.
658: .seealso: `DMSWARM`, `DMSwarmComputeLocalSizeFromOptions()`
659: @*/
660: PetscErrorCode DMSwarmComputeLocalSize(DM sw, PetscInt N, PetscProbFunc density)
661: {
662: DM dm;
663: PetscQuadrature quad;
664: const PetscReal *xq, *wq;
665: PetscReal *n_int;
666: PetscInt *npc_s, *cellid, Ni;
667: PetscReal gmin[3], gmax[3], xi0[3];
668: PetscInt Ns, cStart, cEnd, c, dim, d, Nq, q, Np = 0, p, s;
669: PetscBool simplex;
671: PetscFunctionBegin;
672: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
673: PetscCall(DMSwarmGetCellDM(sw, &dm));
674: PetscCall(DMGetDimension(dm, &dim));
675: PetscCall(DMGetBoundingBox(dm, gmin, gmax));
676: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
677: PetscCall(DMPlexIsSimplex(dm, &simplex));
678: PetscCall(DMGetCoordinatesLocalSetUp(dm));
679: if (simplex) PetscCall(PetscDTStroudConicalQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
680: else PetscCall(PetscDTGaussTensorQuadrature(dim, 1, 5, -1.0, 1.0, &quad));
681: PetscCall(PetscQuadratureGetData(quad, NULL, NULL, &Nq, &xq, &wq));
682: PetscCall(PetscCalloc2(Ns, &n_int, (cEnd - cStart) * Ns, &npc_s));
683: /* Integrate the density function to get the number of particles in each cell */
684: for (d = 0; d < dim; ++d) xi0[d] = -1.0;
685: for (c = 0; c < cEnd - cStart; ++c) {
686: const PetscInt cell = c + cStart;
687: PetscReal v0[3], J[9], invJ[9], detJ, detJp = 2. / (gmax[0] - gmin[0]), xr[3], den;
689: /*Have to transform quadrature points/weights to cell domain*/
690: PetscCall(DMPlexComputeCellGeometryFEM(dm, cell, NULL, v0, J, invJ, &detJ));
691: PetscCall(PetscArrayzero(n_int, Ns));
692: for (q = 0; q < Nq; ++q) {
693: CoordinatesRefToReal(dim, dim, xi0, v0, J, &xq[q * dim], xr);
694: /* Have to transform mesh to domain of definition of PDF, [-1, 1], and weight PDF by |J|/2 */
695: xr[0] = detJp * (xr[0] - gmin[0]) - 1.;
697: for (s = 0; s < Ns; ++s) {
698: PetscCall(density(xr, NULL, &den));
699: n_int[s] += (detJp * den) * (detJ * wq[q]) / (PetscReal)Ns;
700: }
701: }
702: for (s = 0; s < Ns; ++s) {
703: Ni = N;
704: npc_s[c * Ns + s] += (PetscInt)(Ni * n_int[s]);
705: Np += npc_s[c * Ns + s];
706: }
707: }
708: PetscCall(PetscQuadratureDestroy(&quad));
709: PetscCall(DMSwarmSetLocalSizes(sw, Np, 0));
710: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
711: for (c = 0, p = 0; c < cEnd - cStart; ++c) {
712: for (s = 0; s < Ns; ++s) {
713: for (q = 0; q < npc_s[c * Ns + s]; ++q, ++p) cellid[p] = c;
714: }
715: }
716: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_cellid, NULL, NULL, (void **)&cellid));
717: PetscCall(PetscFree2(n_int, npc_s));
718: PetscFunctionReturn(PETSC_SUCCESS);
719: }
721: /*@
722: DMSwarmComputeLocalSizeFromOptions - Compute the local number and distribution of particles based upon a density function determined by options
724: Not Collective
726: Input Parameter:
727: . sw - The `DMSWARM`
729: Level: advanced
731: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`
732: @*/
733: PetscErrorCode DMSwarmComputeLocalSizeFromOptions(DM sw)
734: {
735: PetscProbFunc pdf;
736: const char *prefix;
737: char funcname[PETSC_MAX_PATH_LEN];
738: PetscInt *N, Ns, dim, n;
739: PetscBool flg;
740: PetscMPIInt size, rank;
742: PetscFunctionBegin;
743: PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)sw), &size));
744: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)sw), &rank));
745: PetscCall(PetscCalloc1(size, &N));
746: PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
747: n = size;
748: PetscCall(PetscOptionsIntArray("-dm_swarm_num_particles", "The target number of particles", "", N, &n, NULL));
749: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
750: PetscCall(PetscOptionsInt("-dm_swarm_num_species", "The number of species", "DMSwarmSetNumSpecies", Ns, &Ns, &flg));
751: if (flg) PetscCall(DMSwarmSetNumSpecies(sw, Ns));
752: PetscCall(PetscOptionsString("-dm_swarm_coordinate_function", "Function to determine particle coordinates", "DMSwarmSetCoordinateFunction", funcname, funcname, sizeof(funcname), &flg));
753: PetscOptionsEnd();
754: if (flg) {
755: PetscSimplePointFunc coordFunc;
757: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
758: PetscCall(PetscDLSym(NULL, funcname, (void **)&coordFunc));
759: PetscCheck(coordFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
760: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
761: PetscCall(DMSwarmSetLocalSizes(sw, N[rank] * Ns, 0));
762: PetscCall(DMSwarmSetCoordinateFunction(sw, coordFunc));
763: } else {
764: PetscCall(DMGetDimension(sw, &dim));
765: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
766: PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_coordinate_density", &pdf, NULL, NULL));
767: PetscCall(DMSwarmComputeLocalSize(sw, N[rank], pdf));
768: }
769: PetscCall(PetscFree(N));
770: PetscFunctionReturn(PETSC_SUCCESS);
771: }
773: /*@
774: DMSwarmInitializeCoordinates - Determine the initial coordinates of particles for a PIC method
776: Not Collective
778: Input Parameter:
779: . sw - The `DMSWARM`
781: Level: advanced
783: Note:
784: Currently, we randomly place particles in their assigned cell
786: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeVelocities()`
787: @*/
788: PetscErrorCode DMSwarmInitializeCoordinates(DM sw)
789: {
790: PetscSimplePointFunc coordFunc;
791: PetscScalar *weight;
792: PetscReal *x;
793: PetscInt *species;
794: void *ctx;
795: PetscBool removePoints = PETSC_TRUE;
796: PetscDataType dtype;
797: PetscInt Np, p, Ns, dim, d, bs;
799: PetscFunctionBeginUser;
800: PetscCall(DMGetDimension(sw, &dim));
801: PetscCall(DMSwarmGetLocalSize(sw, &Np));
802: PetscCall(DMSwarmGetNumSpecies(sw, &Ns));
803: PetscCall(DMSwarmGetCoordinateFunction(sw, &coordFunc));
805: PetscCall(DMSwarmGetField(sw, DMSwarmPICField_coor, &bs, &dtype, (void **)&x));
806: PetscCall(DMSwarmGetField(sw, "w_q", &bs, &dtype, (void **)&weight));
807: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
808: if (coordFunc) {
809: PetscCall(DMGetApplicationContext(sw, &ctx));
810: for (p = 0; p < Np; ++p) {
811: PetscScalar X[3];
813: PetscCall((*coordFunc)(dim, 0., NULL, p, X, ctx));
814: for (d = 0; d < dim; ++d) x[p * dim + d] = PetscRealPart(X[d]);
815: weight[p] = 1.0;
816: species[p] = p % Ns;
817: }
818: } else {
819: DM dm;
820: PetscRandom rnd;
821: PetscReal xi0[3];
822: PetscInt cStart, cEnd, c;
824: PetscCall(DMSwarmGetCellDM(sw, &dm));
825: PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
826: PetscCall(DMGetApplicationContext(sw, &ctx));
828: /* Set particle position randomly in cell, set weights to 1 */
829: PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)dm), &rnd));
830: PetscCall(PetscRandomSetInterval(rnd, -1.0, 1.0));
831: PetscCall(PetscRandomSetFromOptions(rnd));
832: PetscCall(DMSwarmSortGetAccess(sw));
833: for (d = 0; d < dim; ++d) xi0[d] = -1.0;
834: for (c = cStart; c < cEnd; ++c) {
835: PetscReal v0[3], J[9], invJ[9], detJ;
836: PetscInt *pidx, Npc, q;
838: PetscCall(DMSwarmSortGetPointsPerCell(sw, c, &Npc, &pidx));
839: PetscCall(DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ));
840: for (q = 0; q < Npc; ++q) {
841: const PetscInt p = pidx[q];
842: PetscReal xref[3];
844: for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &xref[d]));
845: CoordinatesRefToReal(dim, dim, xi0, v0, J, xref, &x[p * dim]);
847: weight[p] = 1.0 / Np;
848: species[p] = p % Ns;
849: }
850: PetscCall(PetscFree(pidx));
851: }
852: PetscCall(PetscRandomDestroy(&rnd));
853: PetscCall(DMSwarmSortRestoreAccess(sw));
854: }
855: PetscCall(DMSwarmRestoreField(sw, DMSwarmPICField_coor, NULL, NULL, (void **)&x));
856: PetscCall(DMSwarmRestoreField(sw, "w_q", NULL, NULL, (void **)&weight));
857: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
859: PetscCall(DMSwarmMigrate(sw, removePoints));
860: PetscCall(DMLocalizeCoordinates(sw));
861: PetscFunctionReturn(PETSC_SUCCESS);
862: }
864: /*@C
865: DMSwarmInitializeVelocities - Set the initial velocities of particles using a distribution.
867: Collective
869: Input Parameters:
870: + sw - The `DMSWARM` object
871: . sampler - A function which uniformly samples the velocity PDF
872: - v0 - The velocity scale for nondimensionalization for each species
874: Level: advanced
876: Note:
877: If `v0` is zero for the first species, all velocities are set to zero. If it is zero for any other species, the effect will be to give that species zero velocity.
879: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocitiesFromOptions()`
880: @*/
881: PetscErrorCode DMSwarmInitializeVelocities(DM sw, PetscProbFunc sampler, const PetscReal v0[])
882: {
883: PetscSimplePointFunc velFunc;
884: PetscReal *v;
885: PetscInt *species;
886: void *ctx;
887: PetscInt dim, Np, p;
889: PetscFunctionBegin;
890: PetscCall(DMSwarmGetVelocityFunction(sw, &velFunc));
892: PetscCall(DMGetDimension(sw, &dim));
893: PetscCall(DMSwarmGetLocalSize(sw, &Np));
894: PetscCall(DMSwarmGetField(sw, "velocity", NULL, NULL, (void **)&v));
895: PetscCall(DMSwarmGetField(sw, "species", NULL, NULL, (void **)&species));
896: if (v0[0] == 0.) {
897: PetscCall(PetscArrayzero(v, Np * dim));
898: } else if (velFunc) {
899: PetscCall(DMGetApplicationContext(sw, &ctx));
900: for (p = 0; p < Np; ++p) {
901: PetscInt s = species[p], d;
902: PetscScalar vel[3];
904: PetscCall((*velFunc)(dim, 0., NULL, p, vel, ctx));
905: for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * PetscRealPart(vel[d]);
906: }
907: } else {
908: PetscRandom rnd;
910: PetscCall(PetscRandomCreate(PetscObjectComm((PetscObject)sw), &rnd));
911: PetscCall(PetscRandomSetInterval(rnd, 0, 1.));
912: PetscCall(PetscRandomSetFromOptions(rnd));
914: for (p = 0; p < Np; ++p) {
915: PetscInt s = species[p], d;
916: PetscReal a[3], vel[3];
918: for (d = 0; d < dim; ++d) PetscCall(PetscRandomGetValueReal(rnd, &a[d]));
919: PetscCall(sampler(a, NULL, vel));
920: for (d = 0; d < dim; ++d) v[p * dim + d] = (v0[s] / v0[0]) * vel[d];
921: }
922: PetscCall(PetscRandomDestroy(&rnd));
923: }
924: PetscCall(DMSwarmRestoreField(sw, "velocity", NULL, NULL, (void **)&v));
925: PetscCall(DMSwarmRestoreField(sw, "species", NULL, NULL, (void **)&species));
926: PetscFunctionReturn(PETSC_SUCCESS);
927: }
929: /*@
930: DMSwarmInitializeVelocitiesFromOptions - Set the initial velocities of particles using a distribution determined from options.
932: Collective
934: Input Parameters:
935: + sw - The `DMSWARM` object
936: - v0 - The velocity scale for nondimensionalization for each species
938: Level: advanced
940: .seealso: `DMSWARM`, `DMSwarmComputeLocalSize()`, `DMSwarmInitializeCoordinates()`, `DMSwarmInitializeVelocities()`
941: @*/
942: PetscErrorCode DMSwarmInitializeVelocitiesFromOptions(DM sw, const PetscReal v0[])
943: {
944: PetscProbFunc sampler;
945: PetscInt dim;
946: const char *prefix;
947: char funcname[PETSC_MAX_PATH_LEN];
948: PetscBool flg;
950: PetscFunctionBegin;
951: PetscOptionsBegin(PetscObjectComm((PetscObject)sw), "", "DMSwarm Options", "DMSWARM");
952: PetscCall(PetscOptionsString("-dm_swarm_velocity_function", "Function to determine particle velocities", "DMSwarmSetVelocityFunction", funcname, funcname, sizeof(funcname), &flg));
953: PetscOptionsEnd();
954: if (flg) {
955: PetscSimplePointFunc velFunc;
957: PetscCall(PetscDLSym(NULL, funcname, (void **)&velFunc));
958: PetscCheck(velFunc, PetscObjectComm((PetscObject)sw), PETSC_ERR_ARG_WRONG, "Could not locate function %s", funcname);
959: PetscCall(DMSwarmSetVelocityFunction(sw, velFunc));
960: }
961: PetscCall(DMGetDimension(sw, &dim));
962: PetscCall(PetscObjectGetOptionsPrefix((PetscObject)sw, &prefix));
963: PetscCall(PetscProbCreateFromOptions(dim, prefix, "-dm_swarm_velocity_density", NULL, NULL, &sampler));
964: PetscCall(DMSwarmInitializeVelocities(sw, sampler, v0));
965: PetscFunctionReturn(PETSC_SUCCESS);
966: }